Hi -- I was wondering if anyone has had any luck with making 40kb jumping libraries using a Fosmid kit. I was looking at this NxSeq 40kb mate pair cloning kit . But really I have no idea what a good kit would be-- the whole process seems like there's a lot of room for mistakes. It will be for Illumina sequencing. Thanks!
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What are you sequencing? You might be better off using long reads (PacBio or Moleculo), which won't be 40Kb but given the recent successes (such as assembling an entire Drosophila chromosome arm)
This is the only kit like it on the market, and it is indeed an involved protocol -- you are first making a cosmid library and then converting it to a sequencing library.
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The genome of interest is highly repetitive (estimated 21% tandem repeats, 42% repetitive). Unfortunately, there isn't a related genome available. I wanted to be able to do structural rearrangement analysis and comparative genomics between different species, which I would think requires a high degree of genome completion.
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Well .. in light of that your choice is going to be limited. Hopefully you can at least do a few SMRTcells on PacBio or other nanopore based technologies would become more generally available this year.
I know that oomycete genomes have been done (and they were certainly problematic back in the day).
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Hi jwag,
Doing a project search on Genohub for exactly 1x coverage on a 1.6 Gb genome yields the following PacBio service providers:
Find and order next-generation sequencing services based on your project specifications. Receive instant quotes with guaranteed quality and turnaround time.
Genomax -- we're hoping too that nanopore tech comes online this year. By chance, are you one of the lucky few that has early access to the MinIon ?
- Genohub
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Originally posted by Genohub View PostGenomax -- we're hoping too that nanopore tech comes online this year. By chance, are you one of the lucky few that has early access to the MinIon ?
Perhaps we should do an anonymous poll and see how many on SeqAnswers got selected?
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